Mitochondria possess their own genome to maintain mitochondrial functions. Modification of mitochondrial DNA (mtDNA) provides important insights into gene functions, disease mechanisms, and therapeutics. However, the available tools for mtDNA editing are relatively limited because of the nature of the unique environment where mtDNA resides and the mechanism of DNA damage repair in mitochondria. With the rapid progress of nuclease and base?editing technologies in recent years, mitochondrially targeted nuclease tools and base editors have been developed, providing powerful tools for mtDNA editing. In this review, we summarize the recent progress of a series of tools developed for targeted editing of animal mtDNA and their applications in biomedicine, focusing on DdCBE (DddA?derived cytosine base editor), and provide a brief outlook on the existing problems and application prospects of mtDNA editing to provide a useful reference for the development of novel tools for mitochondrial genome editing and their wider applications in basic research, disease modeling, and clinical therapeutics.